As mentioned by 'eyeliner' the only way to keep your second Switch clean is to do it with hacdiskmount.
Basically it's creating a dump of the NAND, mounting that with a PC, add the save files and flash back the NAND again.
A lot of risk involved if you don't know what you exactly need to do.
The save files can indeed be retrieved with CheckPoint from the first Switch.
But since CheckPoint only runs on a CFW, you can't use it to copy your save files to the clean Switch.